Land attacks are specifically mentioned as not involving ships. Yet I can't seem to find any part of the rules where it explains that ships are involved in a sea attack - is this just meant to apply to the Poseidon card that lets ships defend as Greeks?

All ancient combat was resolved by soldiers, whether on land or in ships on the water so there is some explanation why it is this way. In the game of Hellas, ships are removed after a successful voyage or converted into soldiers by a God Card or swapped after a battle to the winning side.